Friday, August 30, 2013

It is often assumed that, apart from humans, great apes cannot swim. Many zoos use moats to contain captive chimpanzees and other primates, and it generally works well. It is true that chimpanzees tend to have very low buoyancy (that is, they sink), making drowning a grave risk for them. And indeed, even humans generally require some amount of instruction before they can fend off the dangers of drowning. But is it universally true that apes cannot swim? Renato Bender and Nicole Bender of the University of Witwatersrand, South Africa say no.

Cooper, a male chimpanzee and Suryia, a male orangutan, were both raised in a human environment where they were exposed to swimming pools. You can see footage of the swimming primates below.

A couple of things about this. Suryia was specifically trained to swim, and both animals were given many opportunities to become used to deep water. Ropes strung across the deep end of a pool gave Cooper a safe way to full submerge himself without risking drowning. Finally, it’s only a sample size of two. In other words, these behaviors probably don’t say much if anything about inherent or wild primate behaviors or abilities.

That said Cooper and Suryia do both seem quite comfortable in the water, indicating that there’s no reason wild primates should necessarily have an aversion to deep water. Clearly, they can learn to compensate for low buoyancy by purposeful swimming. Perhaps this is something that zoo keepers should consider in the future.

A. Suryia swimming, view from above. The most characteristic elements are the high range of limb movements, especially from the hind limbs, and the lateral component of hind and front limbs.

B. Suryia swimming, view from the side. The action of the hands and feet during the stroke is shown. Suryia keeps his eyes open under water.

Thursday, August 29, 2013

It has long been known that humans are not the only tool-using animals. A wide variety of animals have been documented using tools, including apes, birds and dolphins. Belonging to the elite tool-using fraternity are a specific group of stone-using Burmese long-tailed macaques (Macaca fascicularis aurea). Although most long-tailed macaques do not use tools, the ones who live on Piak Nam Yai Island in Thailand do. They use stones to crack open the shellfish they find along the coastline.

This kind of tool use is cultural. That is, mothers teach their children how to use the tools. Macaques living in distant locations never learn the trick. This means that tool use can easily be extinguished if the few animals that have those skills die or stop using them. Unfortunately, Michael Gumert from Nanyang Technological University and his colleagues from Kyoto and Chulalongkorn Universities suggest that may be the case for the shellfish-smashing Thai monkeys.

After the 2004 tsunami that devastated the region, much of Thailand was rebuilt so that the island homes of the macaques became much more accessible to humans. For example, people have begun growing rubber and oil palm trees on Piak Nam Yai Island. Fishing, shellfish collection, logging and canal building have all changed the geography of the island and put the monkeys in closer contact with humans and their dogs.

The macaque groups with the most human contact had fewer offspring and spent less time along the coast. The presence of dogs particularly deterred the monkeys from approaching the coastline. Areas with more dogs also had few or no surviving baby macaques.

This has negative consequences for tool use in two ways. If the monkeys can’t get anywhere near the shellfish, there’s no need for them to use tools. And even if they did continue to use their stone hammers, with no offspring, there’s no one to teach the skills to. This does not bode well for uplifting macaques anytime soon.

The authors recommend that wildlife preservation programs take into account the unmolested coastal access macaques need in order to continue their stone-using tradition. While it’s true that the monkeys can adapt to other foods, forestalling their physical extinction, according to the authors, cultural extinction would be nearly as bad.

Wednesday, August 28, 2013

Last week, we learned that we our cities might one day be submerged. However, I like to look on the bright side. If we ever have to move off the land into permanent homes in the oceans, what might our cities look like? I'm glad you asked! Check out these concept homes on io9.Here's my favorite: The Lady Landfill. From the surface, all you'll see are these tiny islands.

But when you dive beneath the surface, you'll find this:

The Lady Landfill was designed by three Serbian architects, Milorad Vidojevic, Jelena Pucarevic and Milica Pihler for the eVolo 2011 Skyscraper Competition. The giant skyscraper would collect and recycle the waste of the Great Pacific Garbage Patch into an energy source.

Tuesday, August 27, 2013

We’re all familiar with the amazing social behavior of ants and bees. But did you know that certain spiders also live in colonies? Not only that, but according to Lena Grinsted and her colleagues from Aarhus University, the social spiders Stegodyphus sarasinorum have distinct personalities.In order for any large social colony to function, members must perform several different types of jobs. For example, some group members might be responsible for gathering or preparing food whereas others might defend the nest. Honeybees sort their tasks by age with each individual progressing through a set schedule of jobs as she matures. However, in Stegodyphus colonies, all the spiders tend to be the same age. How do they decide which among them will be responsible for capturing prey and which for warding off trespassers?One possibility is that the spiders divide up jobs by body size. That is, spiders that happen to be larger than their mates might gravitate to certain jobs. Another is that the spiders have individual preferences or personalities. To test these possibilities, the scientists selected forty spiders out of each of sixteen different nests and painted them, possibly using a technique similar to this method of painting ants. You can see the lovely result below.

Those forty spiders were tested for boldness (how quickly they recovered from a perceived threat), aggression (how they reacted to being poked with a stick) and eagerness to capture prey (how quickly they emerged from the nest to investigate a possible meal and whether they then attacked that prey).

The boldest spiders were the first to rush out of the nest at any sign of prey. They were also the first ones to attack and subdue that prey. Larger spiders were also quick to emerge, but they didn’t necessarily attack first. In fact, size and developmental stage didn’t really make that much difference in determining the spiders’ behavior. Some of them seemed to be inherently bolder or more aggressive.

Because of these differences, the authors conclude that S. sarasinorum have some rudimentary personality traits, though it's not clear what causes the variation in behaviors.Interestingly, there were also colony-wide differences in how the entire spider communities reacted to stimuli. As S. sarasinorum colonies arehighly inbred (siblings tend to remain in the same nest together after having consumed their mother), this could indicate a genetic component to spider personality.Obviously, no one is suggesting that arachnologists begin administering the Myers-Briggs test to their little charges. However, these data do show that spiders do not react as automatons and that there are differences between individual spiders. Needless to say, this was a rather unexpected result. We don't tend to think of such creatures as individuals. This will definitely give me pause the next time I sweep out my house.

Monday, August 26, 2013

Clostridium difficilecauses a bacterial infection that you do not want to get. At best, it causes severe diarrhea, and at worst it can kill you. Normally, C. difficile is held in check by the ‘friendly’ bacteria in a person’s gut, but following antibiotic treatment, the good microbes are often decimated, leaving room for C. difficile to flourish. This means that it’s a particular problem for people who are already trying to recover from a prior illness.

Clostridium difficile

To make matters worse, C. difficile is often antibiotic-resistant. Even when antibiotics appear to clear the infection, it recurs in 20% of individuals. This means that some people need to be treated extremely aggressively to save their lives. But which ones?

As Ray Sheridan of Royal Devon and Exeter NHS Foundation Trust explains:

It's important to get the [right] treatment: too much treatment may see new antibiotic resistant strains emerge; too little and patients might die.

Emma Butt of the University of Exeter and her colleagues have developed an easy way to assess which patients are most at risk for mortality or recurrence.

The scientists began with 186 different variables and narrowed their list down to the four most useful ones:

Friday, August 23, 2013

A few months ago, I published a post about all terrain robots designed with 3D printed legs. Aaron Johnson and Daniel Koditschek from the University of Pennsylvania have used a similar design but gone one better. Their version, the RHex, can hop and leap. But don’t take my word for it. Check out the RHex in action:

RHex is short for ‘robot hexapod’. Depending on how its six legs are activated, the RHex can jump, flip, and even do pull ups (what the scientists refer to as ‘robot Parkour’. The researchers envision someday sending similar robots out into the field to provide surveillance and assistance.

Thursday, August 22, 2013

A great many people were adversely affected by the 2008 recession. Among the people affected were young children, but not just for the reasons you might think. Obviously, children are affected when their parents lose their jobs, their health insurance, and/or their homes. But it turns out that beyond all that, the poor economic climate also made one group of women into harsher mothers.

It’s well documented that mothers parent less well under conditions of stress. This is seen in the primate as well as the human world. The worst environments for parents seem to be those that fluctuate seemingly randomly between bad and good times, suggesting that uncertainty is the worst stressor of all.

There also appear to be genetic components to how well parents handle stress. In particular, the DRD2 gene, which normally encodes part of a dopamine receptor, has a mutant variation (a T in place of a C at a specific site) that results in that individual having fewer dopamine receptors in her brain. In other words, people with the T version have a dampened response to the normal release of the neurotransmitter dopamine.

Dohoon Lee from New York University plus researchers from several other institutions wondered whether there was a correlation between increasingly harsh parenting during bad economic times and having a mutated DRD2 gene. They used the Fragile Families and Child Wellbeing Study as their data source. This study collected information on nearly 5000 children born in 20 large U.S. cities between 1998-2000. The mothers, three quarters of whom were single at the start of the study, were interviewed at the birth of their child, and then again when that child was 1, 3, 5 and 9 years old. Thus, the last data point occurred either right before or soon after the start of the recession. The interviews included ten criteria, half physical and half psychological, to gauge how harshly the children were treated by their mothers. The women also provided saliva samples to determine their DRD2 type.

As the unemployment rate increased, mothers became more harsh with their children. Interestingly, this correlation was not seen with high levels of unemployment, just with changes in those levels, again suggesting that the anticipation of trouble was worse than actual adversity. The affect was much stronger in women with the T version of DRD2 than in those with the C version. Women with the T allele also did not show as much lessening of harshness once times began to improve.

So, if this study is accurate, parenting is adversely affected by poor economic conditions, and women with a particular genotype are especially sensitive to those conditions.

A couple of things about this. First, at this point, we only have an interesting correlation. We can’t yet say that poor economic conditions make mothers treat their children more severely. Second, we definitely can’t say that economic conditions or DRD2 alleles only affect women. This study only interviewed mothers, but there’s no reason to think that men aren’t equally affected.

Wednesday, August 21, 2013

According to projections, if we don't curb climate change, sea levels could rise by as much as 25 feet. The good news is that this won't happen for a couple of millenia. The bad news is that sea level could rise by a foot or two within the next century. Artist Nickolay Lamm shows what would happen in various major cities in a worst case scenario.

Tuesday, August 20, 2013

If you wanted to gather some social data on how citizens move around a large city and how often they encounter each other, how could you do it? Oh, and you’d need your data to be anonymous, so no tracking individual cell phones. One way would be to amass information from transit cards, and that’s just what researchers from the National University of Singapore, the Swiss Federal Institute of Technology, and Wuhan University did.

In Singapore (and many other cities around the world) commuters can use contactless smart cards to pay for their use of public transportation. The user waves the card in front of a smart card reader (in some systems, the card does not have to be removed from the wallet or purse) and the fare is automatically deducted as the person passes by.

Most Singaporeans use the bus for their daily commutes. Thus, the scientists were able to accumulate a dataset including over 20 million bus trips made by nearly 3 million anonymous users.

Among the things the researchers were interested in was how often different pairs of strangers tended to meet. They found that 75% of random pairs of people encountered each other with reliable periodicity. For example, a pair might tend to be on the bus together every 24 or 48 hours (data was only collected on weekdays). Which, of course, makes sense people tend to go to the same place (work, school, etc) every weekday at the same time.

While this all seems like common sense, the study has yielded some useful insights. For example, epidemiologists can use this transit data to see how contagions might spread.

Monday, August 19, 2013

Nine months after suffering from a stroke, a 45 year old Toronto patient started noticing that something very strange was going on. Colors began to elicit strong emotions and tastes. For example, he could now taste the color blue. Not blue items that he put in his mouth, mind you, but just the abstract color. When he saw the color blue, he tasted raspberries. The patient also found a particular shade of blue to be disgusting, and that certain musical tones caused a sense of euphoria. He could not say why these things were suddenly happening to him. His doctors were not so flummoxed. They realized that he had become the second ever confirmed case of acquired synesthesia.

Synesthesia is the cross-firing of the senses. One of the more common forms of synesthesia is called grapheme, or color synesthesia, in which the synesthete sees each letter or number as an exact shade that can be picked out of a color chart. But that’s not the only kind of sensory mix up. Some synesthetes perceive digits to have specific shapes, or even personalities. People with these senses sometimes say that they can do mental arithmetic by merging the shapes and personalities of various numbers into the new shape held by the answer.

Emotional synesthesia, in which digits or objects are paired with specific emotions (blue with disgust) are more rare. To be clear, this is not the same as someone being disgusted by the color blue because they once threw up a blue slushy. The color or shape itself elicits an emotional response independent of past associations.

It’s estimated that a few percent of the population have some form of synesthesia, though it’s hard to quantify either the number of people with the condition or the sorts of phenomenon that synesthesia should include. It definitely seems to be something that people are born with, apart from now two exceptions. Interestingly, the patient’s stroke occurred in his thalamus, which happens to be the same part of the brain affected in the one other case of acquired synesthesia.

Friday, August 16, 2013

This is one of those studies that makes me a bit uneasy. For one thing, the data are still in the preliminary stage. Perhaps more importantly though, if the results do pan out, nobody can really do much about them. The question is whether there’s a correlation between cancer risk and adult female height, and, according to Geoffrey Kabat and his colleagues from the Albert Einstein College of Medicine, the answer is ‘yes’.

Nearly 90,000 women in the Canadian National Breast Screening Study were given self-administered questionnaires asking, among other things, their height and weight. These records were linked to the Canadian Cancer Database and to the National Mortality Database. After about 16 years of follow up, there were close to 6,000 cases of invasive cancers at nineteen different body sites.

The women were divided into five height groups ranging from less than 157 centimeters tall to more than 167 centimeters tall (less than 5 feet 2 inches to greater than 5 feet 5.75 inches). Going from the shortest quintile to the tallest increased a woman’s risk of getting some kind of cancer by 24%. The strongest effect was seen for skin cancers.

There were a few exceptions. Women who were current smokers or had ever used hormonal birth control did not show the correlation between height and cancer risk. The association was also weaker for older women than it was for younger woman.

All this means that we really do not have a clear picture of what’s going on. It will take more studies to prove whether the connection between height and cancer risk is valid, let alone to figure out what there might be causing that relationship. By all means, do not attempt to stunt your daughters’ growth.

Thursday, August 15, 2013

What happens when an organism dies? This question isn’t too hard to answer for single cells, but in a complex multicellular creature, not all cells die at once. How are entire organisms converted from alive to dead? To answer this question, Cassandra Coburn and her colleagues from University College London and other institutions turned to a tiny nematode worm named Caenorhabditis elegans.

There are two ways in which cells die. The first is called apoptosis, or programmed cell death. In multicellular organisms, apoptosis kills isolated cells and is often a necessary part of development. For example, the webbing between our fingers is removed during embryogenesis by apoptosis. The other type of cell death is caused by necrosis. Unlike apoptosis, necrosis is not a normal feature of the cell life cycle. It results from injury (trauma, infection, toxins, etc) and can cause whole tissues or entire organisms to die. Necrotic cell death is characterized by calcium intake and other factors.

C. Elegans alive (left) and dead (right).

Where does C. elegans come in? While normally transparent, C. elegans cells are kind enough to fluoresce bright blue when they die. The authors call this ‘death fluorescence’. Older worms have more of these fluorescent particles than younger worms do. You can tell how close a worm is to the end of its natural life by measuring that fluorescence. However, regardless of age, each worm glows much more brightly at the time of death. Even more intriguing (or morbid, depending on your sensibilities), you can watch a blue wave of death propagate throughout the dying worm.

You can watch a worm turn bright blue and die below.

There is a bright side to all this, even for the worms. When scientists created conditions that would normally kill worms (such as exposing them to heat or cold), they were able to stop the death progression by blocking the necrotic pathway. This only worked in stress-related death though. Blocking necrosis did not help worms who were dying of old age.

Although they don’t turn blue as they die, mammalian cells have similar necrotic pathways. Thus, studying death fluorescence in nematode worms could lead to insights into how more complex creatures progress from life into death.

Wednesday, August 14, 2013

Lonesome George was the last specimen of giant Galapagos tortoises from Pinta Island. Biologists tried to find a mate for him, but sadly, none were to be found. He died, the last of his species, in 2012 at a roughly estimated age of 100 years.The American Museum of Natural History decided to have him preserved for display. They clearly have the taxidermic expertise required, as you can see if you've ever visited their dioramas. The biggest dilemma was to choose the proper pose for this iconic creature. You can see more pictures of Lonesome George here.

Tuesday, August 13, 2013

Variations of the rubber hand illusion have been used in a range of different experiments. But can you use it to give someone a complete body make over? Domna Banakou, Raphaela Groten and Mel Slater from the University of Barcelona show that you can. They used immersive virtual reality (IVR) to turn adults into children.

The authors used IVR to convince 30 adults that they had the body of either a four year old child or of an adult that was scaled down to child-size. Half the time, the virtual body moved synchronously with the volunteer’s body, increasing the illusion of having ownership of that body. In other cases, the virtual body’s movements were disconnected from that of the test subject. You can see an example below:Okay, that didn't look all that convincing. But I'm sure it's different when you're wearing the suit yourself. And in fact, participants did claim to feel personal ownership of their virtual bodies. This was equally true whether that virtual body was that of a child or a tiny adult. However, they overestimated the size of objects (as indicated by holding their hands apart a corresponding distance) more when embodying children’s bodies than when their virtual bodies were small adults. Remember both bodies were the same size, they just had different proportions.

Subjects were also quicker to associate themselves with child-like qualities when they embodied the four year old body, based on implicit association tests. Thus, not only did the participants perceive their environment as if they were really small children, they even reacted like children.

These perceptions disappeared when the movements of the virtual body were asynchronous from the subject’s body. In those experiments, the child’s body and the small adult body were equivalent.

It’s amazing how much we rely on external clues to figure out not only our place in the world, but who we are. For better or worse, people really can be tricked into thinking they’re someone else. This may bode well for humans when we start installing our brains into robot bodies.

Domna Banakou, Raphaela Groten, & Mel Slater (2013). Illusory ownership of a virtual child body causes overestimation of object sizes and implicit attitude changes Proceedings of the National Academy of Sciences of the United States of America DOI: 10.1073/pnas.1306779110.

Stochastic Scientist? What's up with that?

Why the Stochastic Scientist? As I'm sure you all know, 'stochastic' is another word for 'random', which is what I intend for the focus of this blog. Although my formal training is as a molecular biologist, there are many other fields of science that are also fascinating and beautiful. It's my intention to blog about which ever scientific discovery or invention catches my, and hopefully your, fancy.

I also hope to inspire people to learn more about science. By choosing among a huge variety of scientific endeavors, I'll undoubtably hit upon something that will pique my readers' interest.

I guess I could have called my blog 'The Joy of Science', but that wouldn't have been quite so random.